Human mitochondrial DNA (mtDNA) is information-rich, encoding some 22 tRNAs, a 12S and a 16S rRNA, and 13 polypeptides involved in oxidative phosphorylation. No introns have been detected. RNAs are processed by cleavage at tRNA sequences, and polyadenylated posttranscriptionally. In some transcripts, polyadenylation also creates the stop codon, illustrating the parsimony of coding.
A complete prototypical sequence of the human mitochondrial genome has been published. See Anderson et al., Nature 290, 457-465 (1981). The reported sequence in 16,569 base pairs long. There is strand asymmetry in the base compositions, with one strand (Heavy) being relatively G rich, and the other strand (Light) being C rich. The L strand is 30.9% A, 31.2% C, 13.1% G, and 24.7% T. The sequence of the L-strand is numbered arbitrarily from the MboI-5/7 boundary in the D-loop region.
A human cell may have several hundred or more mitochondria, each with more than one copy of mtDNA. Hence each cell actually contains a population of mtDNA molecules. In many individuals, the mtDNA sequence is essentially clonal. However, some individuals carry more than one mtDNA sequence, a condition known as heteroplasmy. The degree of heteroplasmy can vary from tissue to tissue. Also, the rate of replication of mtDNAs can differ and together with random segregation during cell division, can lead to changes in heteroplasmy over time.
Mitochondrial DNA is maternally inherited, and has a mutation rate estimated to be tenfold higher than single copy nuclear DNA (Brown et al., Proc. Natl. Acad. Sci. USA 76, 1967-1971 (1979)). Over 80% of substitutions are transitions (i.e., pyrimidine-pyrimidine or purine-purine).
The determination of a complete human mitochondrial DNA sequence over 15 years ago has had a tremendous influence on studies of human origins and evolution, and the role of mutations in degenerative diseases. Cann et al. Nature 325, 31-36 (1987); Zeviani, et al., Am. J. Hum. Genet. 47, 904-914 (1990); Wallace, Annu. Rev. Biochem. 61, 1175-1212 (1992); Horai et al., Proc. Natl. Acad. Sci. USA 92, 532-536 (1995); Hutchin & Cortopasi, Proc. Natl. Acad. Sci. USA 92, 6892-6895 (1995). Because of the cost and difficulty of conventional sequence analysis, most sequencing studies have focused only on two small hypervariable regions totalling −600 bp. Greenberg et al. Gene 21, 33-49 (1983); Aquardo & Greenberg, Genetics 103, 287-312 (1983).
The present application describes sequencing of the complete mitochondrial genome of several individuals and identifies a large set of polymorphisms.